AutoCloner

Multiple sequence alignment - TraesCS1B01G095800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS1B01G095800	chr1B	100.000	5445	0	0	1	5445	99708808	99714252	0.000000e+00	10056.0
1	TraesCS1B01G095800	chr1B	95.696	395	14	2	3599	3990	99747636	99748030	2.770000e-177	632.0
2	TraesCS1B01G095800	chr1B	88.430	121	14	0	2850	2970	684065786	684065906	4.390000e-31	147.0
3	TraesCS1B01G095800	chr1B	92.308	52	4	0	1165	1216	100308703	100308754	2.100000e-09	75.0
4	TraesCS1B01G095800	chr1D	94.386	1799	46	23	2968	4736	62565920	62567693	0.000000e+00	2712.0
5	TraesCS1B01G095800	chr1D	88.529	1360	110	22	1527	2855	62564578	62565922	0.000000e+00	1605.0
6	TraesCS1B01G095800	chr1D	88.606	1062	30	28	491	1528	62563529	62564523	0.000000e+00	1206.0
7	TraesCS1B01G095800	chr1D	88.952	353	28	3	1	352	62563190	62563532	5.040000e-115	425.0
8	TraesCS1B01G095800	chr1D	86.054	294	32	8	5148	5437	62575422	62575710	1.910000e-79	307.0
9	TraesCS1B01G095800	chr1D	88.514	148	13	2	4733	4878	62567777	62567922	5.610000e-40	176.0
10	TraesCS1B01G095800	chr1D	92.308	52	4	0	1165	1216	62858090	62858141	2.100000e-09	75.0
11	TraesCS1B01G095800	chr1A	93.722	1338	63	12	3580	4903	60539478	60540808	0.000000e+00	1986.0
12	TraesCS1B01G095800	chr1A	87.735	1117	94	27	1764	2855	60537801	60538899	0.000000e+00	1264.0
13	TraesCS1B01G095800	chr1A	91.261	904	47	10	536	1435	60536883	60537758	0.000000e+00	1203.0
14	TraesCS1B01G095800	chr1A	92.857	560	31	8	2974	3528	60538928	60539483	0.000000e+00	804.0
15	TraesCS1B01G095800	chr1A	87.305	512	40	17	4223	4725	60561986	60562481	3.680000e-156	562.0
16	TraesCS1B01G095800	chr1A	97.297	148	4	0	351	498	514129520	514129373	9.050000e-63	252.0
17	TraesCS1B01G095800	chr1A	82.069	145	18	6	4977	5113	60577073	60577217	3.450000e-22	117.0
18	TraesCS1B01G095800	chr6A	98.639	147	2	0	349	495	603645934	603645788	1.500000e-65	261.0
19	TraesCS1B01G095800	chr6A	89.831	118	10	2	2854	2970	897627	897743	3.400000e-32	150.0
20	TraesCS1B01G095800	chr2B	97.386	153	4	0	341	493	629099472	629099624	1.500000e-65	261.0
21	TraesCS1B01G095800	chr2B	89.516	124	12	1	2854	2977	680227413	680227291	7.300000e-34	156.0
22	TraesCS1B01G095800	chr2B	77.778	198	35	8	3627	3818	147285846	147285652	4.460000e-21	113.0
23	TraesCS1B01G095800	chr7B	98.630	146	2	0	348	493	418047495	418047640	5.410000e-65	259.0
24	TraesCS1B01G095800	chr7B	90.000	120	12	0	2851	2970	707590715	707590596	7.300000e-34	156.0
25	TraesCS1B01G095800	chr7B	83.537	164	25	2	1056	1218	640914939	640915101	9.450000e-33	152.0
26	TraesCS1B01G095800	chr7B	89.831	118	12	0	2853	2970	707714975	707715092	9.450000e-33	152.0
27	TraesCS1B01G095800	chr7B	91.228	57	5	0	3762	3818	535506464	535506520	1.630000e-10	78.7
28	TraesCS1B01G095800	chr7B	89.583	48	5	0	1717	1764	39979528	39979481	1.640000e-05	62.1
29	TraesCS1B01G095800	chr7B	100.000	33	0	0	5157	5189	728841086	728841054	1.640000e-05	62.1
30	TraesCS1B01G095800	chr7B	96.970	33	1	0	1732	1764	670286332	670286300	7.620000e-04	56.5
31	TraesCS1B01G095800	chr3B	97.368	152	4	0	342	493	242878731	242878882	5.410000e-65	259.0
32	TraesCS1B01G095800	chr3B	98.621	145	2	0	349	493	458386751	458386895	1.950000e-64	257.0
33	TraesCS1B01G095800	chr3A	97.931	145	3	0	347	491	192849175	192849031	9.050000e-63	252.0
34	TraesCS1B01G095800	chr7D	95.918	147	6	0	347	493	353937879	353937733	7.050000e-59	239.0
35	TraesCS1B01G095800	chr7D	81.277	235	38	4	4208	4440	23101258	23101488	9.310000e-43	185.0
36	TraesCS1B01G095800	chr7D	84.756	164	23	2	1056	1218	577594881	577595043	4.360000e-36	163.0
37	TraesCS1B01G095800	chr7D	90.164	122	12	0	2853	2974	634141465	634141586	5.650000e-35	159.0
38	TraesCS1B01G095800	chr7D	90.000	120	12	0	2851	2970	615416659	615416778	7.300000e-34	156.0
39	TraesCS1B01G095800	chr7D	91.379	58	5	0	3761	3818	506883029	506883086	4.520000e-11	80.5
40	TraesCS1B01G095800	chr7D	96.970	33	1	0	1732	1764	592075582	592075614	7.620000e-04	56.5
41	TraesCS1B01G095800	chr7A	97.037	135	4	0	349	483	679827954	679827820	1.530000e-55	228.0
42	TraesCS1B01G095800	chr7A	85.976	164	21	2	1056	1218	669727875	669728037	2.020000e-39	174.0
43	TraesCS1B01G095800	chr7A	96.970	33	1	0	1732	1764	501064792	501064824	7.620000e-04	56.5
44	TraesCS1B01G095800	chr6B	90.909	121	11	0	2850	2970	708072181	708072301	4.360000e-36	163.0
45	TraesCS1B01G095800	chr6B	89.744	78	5	3	1689	1764	437483009	437482933	4.490000e-16	97.1
46	TraesCS1B01G095800	chr2D	87.500	128	15	1	2850	2977	7396465	7396591	4.390000e-31	147.0
47	TraesCS1B01G095800	chr2D	78.392	199	32	8	3627	3818	95654890	95654696	9.580000e-23	119.0
48	TraesCS1B01G095800	chr2D	78.283	198	34	7	3627	3818	95667597	95667791	9.580000e-23	119.0
49	TraesCS1B01G095800	chr2D	77.778	198	33	8	3628	3818	95684401	95684594	1.600000e-20	111.0
50	TraesCS1B01G095800	chr2A	78.283	198	34	7	3627	3818	94204755	94204561	9.580000e-23	119.0
51	TraesCS1B01G095800	chr2A	72.902	417	84	24	3627	4027	94275989	94276392	3.450000e-22	117.0
52	TraesCS1B01G095800	chr6D	88.312	77	7	2	1689	1764	453809435	453809360	2.090000e-14	91.6
53	TraesCS1B01G095800	chr4D	90.566	53	4	1	1172	1223	81666262	81666210	9.790000e-08	69.4
54	TraesCS1B01G095800	chr4D	97.059	34	1	0	1731	1764	40845310	40845343	2.120000e-04	58.4
55	TraesCS1B01G095800	chr5A	73.301	206	45	9	1018	1218	679738628	679738828	3.520000e-07	67.6
56	TraesCS1B01G095800	chr5D	96.970	33	1	0	1732	1764	534007438	534007406	7.620000e-04	56.5

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS1B01G095800	chr1B	99708808	99714252	5444	False	10056.00	10056	100.00000	1	5445	1	chr1B.!!$F1	5444
1	TraesCS1B01G095800	chr1D	62563190	62567922	4732	False	1224.80	2712	89.79740	1	4878	5	chr1D.!!$F3	4877
2	TraesCS1B01G095800	chr1A	60536883	60540808	3925	False	1314.25	1986	91.39375	536	4903	4	chr1A.!!$F3	4367

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
374	376	0.108615	CTGTTCGGATTCACTCGGCT	60.109	55.000	0.00	0.0	0.00	5.52	F
375	377	0.108804	TGTTCGGATTCACTCGGCTC	60.109	55.000	0.00	0.0	0.00	4.70	F
621	623	0.249398	ATGTGCGTACCACTTCTCCC	59.751	55.000	13.41	0.0	44.92	4.30	F
1709	1796	0.324943	CTCCCTCCGTCCACAAATGT	59.675	55.000	0.00	0.0	0.00	2.71	F
2210	2322	1.078214	GCATCACTGTGCTGCCCTA	60.078	57.895	22.32	0.0	41.82	3.53	F
3743	3896	0.109086	CCTGCTCGACGACATCAAGT	60.109	55.000	0.00	0.0	0.00	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2272	2384	0.108585	AAGACAACGACACCAGGCAT	59.891	50.000	0.00	0.0	0.00	4.40	R
2326	2440	1.810197	TATCGCGCGTATCATCATCG	58.190	50.000	30.98	0.0	0.00	3.84	R
2411	2527	0.798776	CACCCAATCACTCGTGAAGC	59.201	55.000	3.60	0.0	43.58	3.86	R
2545	2662	1.010294	TCCTCCTAATTGGGGTGCCTA	59.990	52.381	8.14	0.0	33.29	3.93	R
3970	4123	0.316841	GGATCACCAGCTCCTCGATC	59.683	60.000	0.00	0.0	35.97	3.69	R
5072	5335	0.036010	CTTGATCTCCACGGCAAGGT	60.036	55.000	0.00	0.0	35.34	3.50	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	37	3.181497	CCAAGCCCAATCAAACATAGTCG	60.181	47.826	0.00	0.00	0.00	4.18
53	55	0.912528	CGTACTCGGCGTCTTAAAGC	59.087	55.000	6.85	0.00	0.00	3.51
70	72	2.604046	AGCGGTGATTGGTAAGCTAG	57.396	50.000	0.00	0.00	32.73	3.42
94	96	4.328712	TGACACGACAATGATGTAAATCCG	59.671	41.667	0.00	0.00	40.74	4.18
109	111	4.882671	AAATCCGTGCACATTCTACATC	57.117	40.909	18.64	0.00	0.00	3.06
112	114	3.261580	TCCGTGCACATTCTACATCAAG	58.738	45.455	18.64	0.00	0.00	3.02
135	137	3.629398	ACCATGAATCATTCTTTCTCGGC	59.371	43.478	0.00	0.00	0.00	5.54
197	199	8.367396	CGAATGTCATGTGTAAATTTCAACATG	58.633	33.333	25.88	25.88	37.05	3.21
198	200	9.195411	GAATGTCATGTGTAAATTTCAACATGT	57.805	29.630	28.11	18.05	37.04	3.21
199	201	7.927305	TGTCATGTGTAAATTTCAACATGTG	57.073	32.000	28.11	16.94	37.04	3.21
200	202	7.710896	TGTCATGTGTAAATTTCAACATGTGA	58.289	30.769	28.11	19.70	37.04	3.58
201	203	8.358895	TGTCATGTGTAAATTTCAACATGTGAT	58.641	29.630	28.11	7.68	35.70	3.06
202	204	8.641155	GTCATGTGTAAATTTCAACATGTGATG	58.359	33.333	28.11	15.60	35.70	3.07
204	206	8.641155	CATGTGTAAATTTCAACATGTGATGTC	58.359	33.333	24.63	3.84	44.07	3.06
227	229	3.168292	TCTGCATCATCCTACCATCGAT	58.832	45.455	0.00	0.00	0.00	3.59
264	266	2.493278	CCGTGCCCTGAAATTTGATTCT	59.507	45.455	0.00	0.00	0.00	2.40
266	268	3.191162	CGTGCCCTGAAATTTGATTCTGA	59.809	43.478	0.00	0.00	31.96	3.27
267	269	4.673580	CGTGCCCTGAAATTTGATTCTGAG	60.674	45.833	0.00	0.00	31.96	3.35
271	273	6.891361	TGCCCTGAAATTTGATTCTGAGAATA	59.109	34.615	7.82	0.00	31.96	1.75
297	299	9.877178	ATTTTTACCATATGTAAATTGCCGAAA	57.123	25.926	1.24	0.00	46.11	3.46
298	300	9.877178	TTTTTACCATATGTAAATTGCCGAAAT	57.123	25.926	1.24	0.00	46.11	2.17
299	301	9.877178	TTTTACCATATGTAAATTGCCGAAATT	57.123	25.926	1.24	0.00	46.11	1.82
340	342	4.877282	TCCGTGGATCAAACCAAAATTTC	58.123	39.130	0.00	0.00	41.87	2.17
344	346	5.299949	GTGGATCAAACCAAAATTTCTGCT	58.700	37.500	0.00	0.00	41.87	4.24
348	350	5.596836	TCAAACCAAAATTTCTGCTGACT	57.403	34.783	0.00	0.00	0.00	3.41

Showing 1 to 25 of 568 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	5.792741	TGTTTGATTGGGCTTGGATAAAAG	58.207	37.500	0.00	0.00	0.00	2.27
35	37	0.912528	CGCTTTAAGACGCCGAGTAC	59.087	55.000	0.00	0.00	0.00	2.73
53	55	3.187700	GTCACTAGCTTACCAATCACCG	58.812	50.000	0.00	0.00	0.00	4.94
70	72	5.560148	GGATTTACATCATTGTCGTGTCAC	58.440	41.667	0.00	0.00	37.28	3.67
94	96	4.002982	TGGTCTTGATGTAGAATGTGCAC	58.997	43.478	10.75	10.75	0.00	4.57
109	111	6.457934	CCGAGAAAGAATGATTCATGGTCTTG	60.458	42.308	12.26	7.55	0.00	3.02
112	114	4.260948	GCCGAGAAAGAATGATTCATGGTC	60.261	45.833	8.03	0.00	0.00	4.02
151	153	6.928979	TTCGGTTACACATTTCTTGAAAGA	57.071	33.333	2.25	0.00	0.00	2.52
152	154	7.138736	ACATTCGGTTACACATTTCTTGAAAG	58.861	34.615	2.25	0.00	0.00	2.62
199	201	4.252073	GGTAGGATGATGCAGATGACATC	58.748	47.826	7.39	7.39	43.46	3.06
200	202	3.649502	TGGTAGGATGATGCAGATGACAT	59.350	43.478	0.00	0.00	0.00	3.06
201	203	3.040477	TGGTAGGATGATGCAGATGACA	58.960	45.455	0.00	0.00	0.00	3.58
202	204	3.758755	TGGTAGGATGATGCAGATGAC	57.241	47.619	0.00	0.00	0.00	3.06
203	205	3.056322	CGATGGTAGGATGATGCAGATGA	60.056	47.826	0.00	0.00	0.00	2.92
204	206	3.056322	TCGATGGTAGGATGATGCAGATG	60.056	47.826	0.00	0.00	0.00	2.90
227	229	3.045142	GGGTCCGACACGACAAGA	58.955	61.111	0.00	0.00	34.24	3.02
278	280	5.177327	GGCAATTTCGGCAATTTACATATGG	59.823	40.000	7.80	0.00	32.24	2.74
280	282	4.981674	CGGCAATTTCGGCAATTTACATAT	59.018	37.500	0.00	0.00	32.24	1.78
291	293	1.799916	CCGTTTCGGCAATTTCGGC	60.800	57.895	0.00	0.00	41.17	5.54
292	294	4.450955	CCGTTTCGGCAATTTCGG	57.549	55.556	0.00	0.00	41.17	4.30
314	316	6.597832	ATTTTGGTTTGATCCACGGAATTA	57.402	33.333	0.00	0.00	37.20	1.40
316	318	5.482163	AATTTTGGTTTGATCCACGGAAT	57.518	34.783	0.00	0.00	37.20	3.01
340	342	2.079925	GAACAGGGCTTTAGTCAGCAG	58.920	52.381	0.00	0.00	42.10	4.24
344	346	1.344065	TCCGAACAGGGCTTTAGTCA	58.656	50.000	0.00	0.00	41.52	3.41
348	350	2.304761	AGTGAATCCGAACAGGGCTTTA	59.695	45.455	0.00	0.00	41.52	1.85

Showing 1 to 25 of 580 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.